ENCODE
Assays and standards Glossary File formats Software tools Pipelines Data organization Release policy Schemas Help Using the portal Cart REST API Citing ENCODE FAQ Project Overview …
Search – ENCODE
Project: ENCODE Library construction method: capped RNA enrichment Experiment ENCSR841GXY released PRO-cap in peripheral blood mononuclear cell Homo sapiens peripheral blood …
Access to ENCODE data
All data generated by the ENCODE consortium is submitted to the DCC and available from the ENCODE portal (http://www.encodeproject.org). The data are reviewed for quality and released to …
Data standards – ENCODE
The ENCODE Consortium has adopted shared experimental guidelines for the most common ENCODE assays. The guidelines have evolved over time as technologies have changed, and current …
eCLIP Data Standards – ENCODE
Antibodies must be characterized according to standards set by the ENCODE Consortium. Please see the linked documents for transcription factor standards (May 2016), histone modification and …
ATAC-seq Data Standards and Processing Pipeline – ENCODE
The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment.
FAQ – ENCODE
The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells …
ENCODE Encyclopedia
The ENCODE Project aims to map all functional elements of the human and mouse genomes. Progress toward this goal has involved over ten thousand epigenomic experiments utilizing a wide array of …
Data Processing Pipelines – ENCODE
The ENCODE Data Coordinating Center has developed data processing pipelines for major assay types generated by the project: RNA-seq, RAMPAGE 1, ChIP-seq, DNase-seq, ATAC-seq 2 , and WGBS.
Histone ChIP-seq Data Standards and Processing Pipeline (ENCODE 4) …
The ENCODE consortium has developed two analysis pipelines to study two different classes of protein-chromatin interactions. The histone ChIP-seq pipeline, described here, is suitable for proteins that …